Identification of human orofacial enhancers and their role in orofacial clefts

人类口面部增强剂的鉴定及其在口面部裂隙中的作用

基本信息

批准号：
9057242
负责人：
Justin Lee Cotney
金额：
$ 24.9万
依托单位：
UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-05-01 至 2018-04-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9057242
关键词：
Address Adult Affect Award Binding Biochemical Biochemistry Biological Assay Birth Branchial arch structure ChIP-seq Chromatin Chromosomes Cleft Lip Code Computing Methodologies Conceptions Congenital Abnormality DNA Data Data Set Defect Development Development Plans Developmental Biology Developmental Gene Disease Elements Embryo Embryonic Development Enhancers Evolution Face FaceBase Faculty Family Functional disorder Future Gene Expression Gene Expression Profile Gene Expression Regulation Gene Targeting Genes Genetic Genetic Markers Genome Goals Graduate Degree Hand Health Heritability Human Human Genetics Human Genome Human Identifications Individual Institution Instruction Jaw Knock-in Mouse Letters Lifting Limb structure Linkage Disequilibrium Live Birth Measures Mentors Methods Mitochondria Molecular Biology Molecular Conformation Mus Mutate Outcome Palate Parents Pathway interactions Patients Pattern Phase Positioning Attribute Postdoctoral Fellow Public Health Publishing Regulator Genes Regulatory Element Research Research Personnel Resources Role Sampling Signal Transduction Single Nucleotide Polymorphism Staging Structure Techniques Testing Therapeutic Tissues Training Transgenic Mice Trust Universities Untranslated RNA Variant Work biobank career development cleft lip and palate cohesin craniofacial embryo tissue falls foot functional genomics genome wide association study genome-wide histone modification human data human disease medical schools member novel orofacial orofacial cleft palatal shelves prevent research study spatiotemporal targeted sequencing transcription factor transcriptome sequencing

项目摘要

DESCRIPTION (provided by applicant): Orofacial clefts are one of the most commonly occurring human birth defects, yet the underlying causes remain largely unknown. Genome wide association studies indicate heritability for such defects, however the vast majority of associations fall outside of genes suggesting defective gene regulation is a major contributor. The proposed work seeks to identify the genetic causes of nonsyndromic cleft lip and palate (NSCLP) by identifying and characterizing gene regulatory sequences that are active in early human orofacial development and disrupted in affected individuals. Preliminary research using functional genomics methods directly in human embryonic tissue has identified thousands of potential orofacial regulatory sequences, including several that are in linkage disequilibrium with single nucleotide polymorphisms strongly associated with NSCLP. This "Pathway to Independence" award application includes a mentored career development plan for transition of the candidate, Dr. Justin Cotney, into an independent investigator, as well an accompanying research plan describing the proposed experiments on identification and characterization of disease-associated variants in gene regulatory sequences. The candidate, Dr. Cotney, is a postdoctoral fellow at Yale University School of Medicine, in the lab of Dr. James Noonan in the Department of Genetics. The work leading to his graduate degree in Genetics and Molecular Biology at Emory University was conducted in the lab of Dr. Gerald Shadel in the Department of Biochemistry at Emory and Department of Genetics at Yale. There he focused on understanding the contributions of two members of a novel class of transcription factors to human mitochondrial gene expression and retrograde signaling. In the Noonan lab, Dr. Cotney applied biochemical and computational methods to identify gene regulatory sequences directly in embryonic limb tissue that have contributed to human-specific evolution of the hand and foot. The techniques and computational methods to address these evolutionary questions in embryonic development can be adapted to understand gene regulation in any developing tissue, placing Dr. Cotney in a unique position to investigate the causes of NSCLP. The mentoring and career development plan detailed within will supplement his background in basic molecular biology and functional genomics with additional training and instruction in statistical genetics and human orofacial development. Dr. Cotney's goal is to become a faculty member in an interdisciplinary bioscience, developmental biology, or similar department at an academic institution, in which he can research the role of dysfunction of developmental gene regulation in common human diseases. The research plan will leverage Dr. Cotney's expertise in functionally profiling embryonic tissue to identify gene regulatory sequences that are active during the formation of pharyngeal arches to fusion of palates and facial structures. The project further proposes to determine which of these activated regulatory elements are burdened with variants and structural changes in NSCLP patients and identify the consequences of disrupted developmental gene regulation. The identification of gene regulatory networks that are commonly perturbed in NSCLP patients will provide genetic markers that can predict the occurrence of these defects and provide targets for future preventative or therapeutic measures. Alleviating the impact of orofacial clefts and preventing their occurrence will increase global public health and lift a large financial burden currently faced by affected individuals and their families.

描述（由申请人提供）：口面裂口是最常见的人类出生缺陷之一，但基本原因仍然很少知道。基因组广泛的关联研究表明这种缺陷的遗传力，但是绝大多数关联属于基因，表明基因调节缺陷是主要的贡献者。拟议的工作旨在通过鉴定和表征活性在早期人类口交发展并在受影响的个体中破坏的基因调节序列来确定非蛋白质裂唇裂（NSCLP）的遗传原因（NSCLP）。直接在人类胚胎组织中使用功能基因组方法的初步研究已经确定了数千个潜在的口面调节序列，包括几种与链接的序列单核苷酸多态性与NSCLP密切相关。这种“通往独立途径”奖项的申请包括一项指导的职业发展计划，用于过渡候选人贾斯汀·科特尼（Justin Cotney）博士为独立研究者，以及随附的研究计划，描述了有关基因调节序列中疾病相关变体的拟议实验。候选人Cotney博士是耶鲁大学医学院的博士后研究员，在遗传学系詹姆斯·诺南（James Noonan）博士的实验室中。导致埃默里大学遗传学和分子生物学研究生学位的工作是在埃默里（Emory）生物化学系和耶鲁大学遗传学系的杰拉尔德·沙德尔（Gerald Shadel）博士实验室进行的。在那里，他专注于理解一类新的转录因子的两个成员对人线粒体基因表达和逆行信号的贡献。在Noonan实验室中，Cotney博士应用了生化和计算方法，以直接在胚胎肢体组织中鉴定基因调节序列，这导致了手和脚的人类特异性演化。可以调整解决胚胎发育中这些进化问题的技术和计算方法，以了解任何发育中的组织中的基因调节，使科特尼博士处于独特的位置，以研究NSCLP的原因。详细介绍的指导和职业发展计划将补充他在基本分子生物学和功能基因组学方面的背景，并在统计遗传学和人类的口面发展中进行其他培训和指导。科特尼博士的目标是成为学术机构跨学科生物科学，发展生物学或类似部门的教职员工，在该学术机构中，他可以研究共同疾病中发育基因调节功能障碍的作用。该研究计划将利用科特尼博士在功能分析胚胎组织方面的专业知识，以识别在形成咽弓过程中活跃的基因调节序列，以融合口感和面部结构。该项目进一步建议确定这些激活的调节元素中的哪个负担到NSCLP患者的变异和结构变化，并确定破坏的发育基因调控的后果。 NSCLP患者通常会扰动的基因调节网络的鉴定将提供遗传标记，以预测这些缺陷的发生，并为未来的预防或治疗方法提供目标。减轻口腔裂缝的影响并防止其发生的影响将增加全球公共卫生，并增加受影响个人及其家人目前面临的巨大财务负担。